Otitis media is the second most common infection in children and the leading cause for seeking medical advice. Indigenous populations such as the Inuits, indigenous Australians and American Indians have a very high prevalence of otitis media and are considered to be high-risk populations. Streptococcus pneumoniae, one of the three main bacterial causes of otitis media, colonises the nasopharynx prior to disease development. In high-risk populations, early acquisition of high bacterial loads increases the prevalence of otitis media. In these settings, current treatment strategies are insufficient. Vaccination is effective against invasive pneumococcal infection but has a limited impact on otitis media. Decreasing the bacterial loads of otitis media pathogens and/or colonising the nasopharynx with beneficial bacteria may reduce the prevalence of otitis media. Probiotics are live microorganisms that offer health benefits by modulating the microbial community and enhancing host immunity. The available data suggest that probiotics may be beneficial in otitis media. This review discusses the potential use of probiotics to reduce pathogen colonisation and decrease the prevalence of otitis media, providing justification for further investigation.